Dear Amber !
It is working good !
I also tried similar like this for finding the intermolecular interactions
I used the following script !
trajin ../md1.mdcrd
center :1-6
image familiar
hbond MyHB :1-6 out try.dat dist 3.5 angle 120 avgout tryavghb.dat
nointramol series solventacceptor :WAT.O solvent donor :WAT solvout
sovent_avg.dat bridgeout bridge.data
run
writedata solutehb.dat MyHB[solutehb]
writedata solventhb.dat MyHB[solventhb]
lifetime MyHB[solutehb] out solute.lifetime.dat
lifetime MyHB[solventhb] out solvent.lifetime.dat
runanalysis
the script is not working I made mistake on defining the water donor or
acceptor molecules
could any one help me to fix this
thank you
On Wed, Jun 24, 2015 at 2:48 PM, Lara rajam <lara.4884.gmail.com> wrote:
> Dear Amber
>
> I tried calculating the hydrogen bond from cpptraj
>
> I am able to do the possible hydrogen bond between the solute residues 1-6
> as below
>
> trajin ../md1.mdcrd
>
> center :1-6
>
> image familiar
>
> hbond distance 3.5 angle 120.0 :1-6 out 3.5_nhb.dat avgout 3.5_avghb.dat
>
>
> but I am not able to do the life time for the same i tried as below
>
>
> trajin ../md1.mdcrd
>
> center :1-6
>
> image familiar
>
> hbond distance 3.5 angle 120.0 :1-6 out 3.5_nhb.dat avgout 3.5_avghb.dat
> series lifetime.data
>
>
> since the series word should be added with the following file name
>
>
> not able to get the out file ..
>
>
> let me know what error I am doing so that it can be fixed
>
>
> thank you
>
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Received on Wed Jun 24 2015 - 14:00:02 PDT
